Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis
Gillet, Ludovic C., Navarro, Pedro, Tate, Stephen, Röst, Hannes, Selevsek, Nathalie, Reiter, Lukas, Bonner, Ron, Aebersold, Ruedi
Published in Molecular & cellular proteomics (01.06.2012)
Published in Molecular & cellular proteomics (01.06.2012)
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Journal Article
Building high-quality assay libraries for targeted analysis of SWATH MS data
Schubert, Olga T, Gillet, Ludovic C, Collins, Ben C, Navarro, Pedro, Rosenberger, George, Wolski, Witold E, Lam, Henry, Amodei, Dario, Mallick, Parag, MacLean, Brendan, Aebersold, Ruedi
Published in Nature protocols (01.03.2015)
Published in Nature protocols (01.03.2015)
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Journal Article
Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system
Collins, Ben C, Gillet, Ludovic C, Rosenberger, George, Röst, Hannes L, Vichalkovski, Anton, Gstaiger, Matthias, Aebersold, Ruedi
Published in Nature methods (01.12.2013)
Published in Nature methods (01.12.2013)
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Journal Article
Quantitative variability of 342 plasma proteins in a human twin population
Liu, Yansheng, Buil, Alfonso, Collins, Ben C, Gillet, Ludovic CJ, Blum, Lorenz C, Cheng, Lin‐Yang, Vitek, Olga, Mouritsen, Jeppe, Lachance, Genevieve, Spector, Tim D, Dermitzakis, Emmanouil T, Aebersold, Ruedi
Published in Molecular systems biology (01.02.2015)
Published in Molecular systems biology (01.02.2015)
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Journal Article
Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis
Schubert, Olga T., Ludwig, Christina, Kogadeeva, Maria, Zimmermann, Michael, Rosenberger, George, Gengenbacher, Martin, Gillet, Ludovic C., Collins, Ben C., Röst, Hannes L., Kaufmann, Stefan H.E., Sauer, Uwe, Aebersold, Ruedi
Published in Cell host & microbe (08.07.2015)
Published in Cell host & microbe (08.07.2015)
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Journal Article
Reproducible and Consistent Quantification of the Saccharomyces cerevisiae Proteome by SWATH-mass spectrometry
Selevsek, Nathalie, Chang, Ching-Yun, Gillet, Ludovic C., Navarro, Pedro, Bernhardt, Oliver M., Reiter, Lukas, Cheng, Lin-Yang, Vitek, Olga, Aebersold, Ruedi
Published in Molecular & cellular proteomics (01.03.2015)
Published in Molecular & cellular proteomics (01.03.2015)
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Journal Article
Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness
Liu, Yansheng, Chen, Jing, Sethi, Atul, Li, Qing K., Chen, Lijun, Collins, Ben, Gillet, Ludovic C.J., Wollscheid, Bernd, Zhang, Hui, Aebersold, Ruedi
Published in Molecular & cellular proteomics (01.07.2014)
Published in Molecular & cellular proteomics (01.07.2014)
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Journal Article
USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit
Montellese, Christian, van den Heuvel, Jasmin, Ashiono, Caroline, Dörner, Kerstin, Melnik, André, Jonas, Stefanie, Zemp, Ivo, Picotti, Paola, Gillet, Ludovic C, Kutay, Ulrike
Published in eLife (04.03.2020)
Published in eLife (04.03.2020)
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Journal Article
Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36
van den Heuvel, Jasmin, Ashiono, Caroline, Gillet, Ludovic C, Dörner, Kerstin, Wyler, Emanuel, Zemp, Ivo, Kutay, Ulrike
Published in eLife (28.07.2021)
Published in eLife (28.07.2021)
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Journal Article
Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization
King, Grant A, Wettstein, Rahel, Varberg, Joseph M, Chetlapalli, Keerthana, Walsh, Madison E, Gillet, Ludovic C J, Hernández-Armenta, Claudia, Beltrao, Pedro, Aebersold, Ruedi, Jaspersen, Sue L, Matos, Joao, Ünal, Elçin
Published in The Journal of cell biology (06.02.2023)
Published in The Journal of cell biology (06.02.2023)
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Journal Article
The GTPase Nog1 co-ordinates the assembly, maturation and quality control of distant ribosomal functional centers
Klingauf-Nerurkar, Purnima, Gillet, Ludovic C, Portugal-Calisto, Daniela, Oborská-Oplová, Michaela, Jäger, Martin, Schubert, Olga T, Pisano, Agnese, Peña, Cohue, Rao, Sanjana, Altvater, Martin, Chang, Yiming, Aebersold, Ruedi, Panse, Vikram G
Published in eLife (07.01.2020)
Published in eLife (07.01.2020)
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Journal Article
Phosphoproteomic analyses reveal novel cross‐modulation mechanisms between two signaling pathways in yeast
Vaga, Stefania, Bernardo‐Faura, Marti, Cokelaer, Thomas, Maiolica, Alessio, Barnes, Christopher A, Gillet, Ludovic C, Hegemann, Björn, van Drogen, Frank, Sharifian, Hoda, Klipp, Edda, Peter, Matthias, Saez‐Rodriguez, Julio, Aebersold, Ruedi
Published in Molecular systems biology (01.12.2014)
Published in Molecular systems biology (01.12.2014)
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Journal Article
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps
Guo, Tiannan, Kouvonen, Petri, Koh, Ching Chiek, Gillet, Ludovic C, Wolski, Witold E, Röst, Hannes L, Rosenberger, George, Collins, Ben C, Blum, Lorenz C, Gillessen, Silke, Joerger, Markus, Jochum, Wolfram, Aebersold, Ruedi
Published in Nature medicine (01.04.2015)
Published in Nature medicine (01.04.2015)
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Journal Article
A multicenter study benchmarks software tools for label-free proteome quantification
Navarro, Pedro, Kuharev, Jörg, Gillet, Ludovic C, Bernhardt, Oliver M, MacLean, Brendan, Röst, Hannes L, Tate, Stephen A, Tsou, Chih-Chiang, Reiter, Lukas, Distler, Ute, Rosenberger, George, Perez-Riverol, Yasset, Nesvizhskii, Alexey I, Aebersold, Ruedi, Tenzer, Stefan
Published in Nature biotechnology (01.11.2016)
Published in Nature biotechnology (01.11.2016)
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Journal Article
Conserved Peptide Fragmentation as a Benchmarking Tool for Mass Spectrometers and a Discriminating Feature for Targeted Proteomics
Toprak, Umut H., Gillet, Ludovic C., Maiolica, Alessio, Navarro, Pedro, Leitner, Alexander, Aebersold, Ruedi
Published in Molecular & cellular proteomics (01.08.2014)
Published in Molecular & cellular proteomics (01.08.2014)
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Journal Article
Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry[S]
Amon, Sabine, Meier-Abt, Fabienne, Gillet, Ludovic C., Dimitrieva, Slavica, Theocharides, Alexandre P.A., Manz, Markus G., Aebersold, Ruedi
Published in Molecular & cellular proteomics (01.07.2019)
Published in Molecular & cellular proteomics (01.07.2019)
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